<tool id="minfi_rset" name="Minfi rset" version="@MINFI_VERSION@">
    <description>store Beta values and/or M values</description>
      <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        Rscript '$read_rset_script'
     ]]>
   </command>
 <configfiles>
      <configfile name="read_rset_script">
   <![CDATA[
require("minfi", quietly = TRUE)
MSet <- get(load('$mset'))

RSet <- ratioConvert(MSet, what = "both", keepCN = TRUE)

save(RSet,file = '$rset')  
    ]]> </configfile>
        </configfiles>
  <inputs>
        <param type="data" name="mset" format="rdata" label="MethylSet" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
location."/>
    </inputs>
    <outputs>
        <data name="rset" format="rdata" label="RatioSet"/>
    </outputs>
    <tests>
        <test>
            <param name="mset" value="MethylSet.rdata"/>
            <output name="rset" file="RatioSet.rdata"/>
        </test>
    </tests>
    <help><![CDATA[
        RSet class holds preprocessed data for Illumina methylation microarrays. It contains respectively the Beta value matrix, M value matrix and the Copy Number matrix.
    ]]></help>
    <expand macro="citations" />
</tool>